General information for g10729.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as AP-2 complex subunit sigma.
Parent gene
- The parent gene g10729 is located on chr_1: 11615180..11616994 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_1 | g10729 | g10729.t3 | TSS | g10729.t3 | 11614560 | 11614560 |
| chr_1 | g10729 | g10729.t3 | isoform | g10729.t3 | 11614633 | 11615180 |
| chr_1 | g10729 | g10729.t3 | exon | g10729.t3.exon1 | 11614633 | 11614852 |
| chr_1 | g10729 | g10729.t3 | cds | g10729.t3.CDS1 | 11614760 | 11614852 |
| chr_1 | g10729 | g10729.t3 | exon | g10729.t3.exon2 | 11614905 | 11615180 |
| chr_1 | g10729 | g10729.t3 | cds | g10729.t3.CDS2 | 11614905 | 11615180 |
| chr_1 | g10729 | g10729.t3 | TTS | g10729.t3 | 11615401 | 11615401 |
Sequences
>g10729.t3 Gene=g10729 Length=496
ATGGTAAGAAATAGATTACAATATTGTTCAAAGATGTACTTTAACTTAGAAGAATTTTTT
AATTTTATAGATTCGTTTTATTTTGATTCAAAACCGTGCAGGAAAAACTAGATTAGCAAA
ATGGTATATGCAATTCGATGACGATGAAAAACAAAAATTAATTGAAGAAGTTCATGCTGT
AGTCACTGTCAGAGATGCTAAACATACCAATTTTGTTGAATTTCGCAACTTTAAGATTGT
CTATAGACGATATGCTGGATTATATTTCTGTATATGTGTTGACGTTAATGATAACAACTT
GTGCTATCTCGAAGCGATTCACAATTTCGTGGAAGTTTTAAATGAGTATTTCCATAATGT
TTGTGAATTGGATCTGGTATTCAATTTTTATAAAGTTTATACTGTTGTCGATGAGATGTT
TTTAGCAGGCGAGATTAGAGAGACTTCACAAACAAAAGTCCTCAAGCAGCTGCTTACACT
CAATTCATTAGACTAA
>g10729.t3 Gene=g10729 Length=122
MQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIVYRRYAGLYFCICVDVNDNNLCY
LEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKQLLTLNS
LD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g10729.t3 | Gene3D | G3DSA:3.30.450.60 | - | 1 | 122 | 3.0E-44 |
| 2 | g10729.t3 | PANTHER | PTHR11753:SF6 | AP-2 COMPLEX SUBUNIT SIGMA | 1 | 121 | 1.1E-62 |
| 3 | g10729.t3 | PANTHER | PTHR11753 | ADAPTOR COMPLEXES SMALL SUBUNIT FAMILY | 1 | 121 | 1.1E-62 |
| 7 | g10729.t3 | PIRSF | PIRSF015588 | AP_complex_sigma | 1 | 122 | 2.1E-51 |
| 1 | g10729.t3 | Pfam | PF01217 | Clathrin adaptor complex small chain | 2 | 121 | 1.5E-50 |
| 5 | g10729.t3 | ProSitePatterns | PS00989 | Clathrin adaptor complexes small chain signature. | 37 | 47 | - |
| 4 | g10729.t3 | SUPERFAMILY | SSF64356 | SNARE-like | 5 | 116 | 5.04E-33 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006886 | intracellular protein transport | BP |
| GO:0030117 | membrane coat | CC |
| GO:0072583 | clathrin-dependent endocytosis | BP |
| GO:0035615 | clathrin adaptor activity | MF |
| GO:0030122 | AP-2 adaptor complex | CC |
| GO:0015031 | protein transport | BP |
| GO:0016192 | vesicle-mediated transport | BP |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
